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<li class="navelem"><b>claragenomics</b></li><li class="navelem"><b>cudaaligner</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a></li>  </ul>
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<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="classclaragenomics_1_1cudaaligner_1_1Aligner-members.html">List of all members</a>  </div>
  <div class="headertitle">
<div class="title">claragenomics::cudaaligner::Aligner Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span><div class="ingroups"><a class="el" href="group__cudaaligner.html">CUDA Aligner package</a></div></div>  </div>
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<p><code>#include &lt;<a class="el" href="aligner_8hpp_source.html">aligner.hpp</a>&gt;</code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
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virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#aaae329eae2ed3e364db643163755e987">~Aligner</a> ()=default</td></tr>
<tr class="memdesc:aaae329eae2ed3e364db643163755e987"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor for <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a>. <br /></td></tr>
<tr class="separator:aaae329eae2ed3e364db643163755e987"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8b3c20782b9eaa4c2219fb7ff51772db"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a8b3c20782b9eaa4c2219fb7ff51772db">align_all</a> ()=0</td></tr>
<tr class="memdesc:a8b3c20782b9eaa4c2219fb7ff51772db"><td class="mdescLeft">&#160;</td><td class="mdescRight">Launch CUDA accelerated alignment.  <a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a8b3c20782b9eaa4c2219fb7ff51772db">More...</a><br /></td></tr>
<tr class="separator:a8b3c20782b9eaa4c2219fb7ff51772db"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac929b7ba836dfac74d8975f652563482"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">sync_alignments</a> ()=0</td></tr>
<tr class="memdesc:ac929b7ba836dfac74d8975f652563482"><td class="mdescLeft">&#160;</td><td class="mdescRight">Waits for CUDA accelerated alignment to finish.  <a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">More...</a><br /></td></tr>
<tr class="separator:ac929b7ba836dfac74d8975f652563482"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:adc32085da2b5681f0045d05c43a35f92"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">add_alignment</a> (const char *query, int32_t query_length, const char *target, int32_t target_length)=0</td></tr>
<tr class="memdesc:adc32085da2b5681f0045d05c43a35f92"><td class="mdescLeft">&#160;</td><td class="mdescRight">Add new alignment object. Only strings with characters from the alphabet [ACGT] are guaranteed to provide correct results.  <a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">More...</a><br /></td></tr>
<tr class="separator:adc32085da2b5681f0045d05c43a35f92"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1d775f9821ce3ecdcdc67cb07f35a4d8"><td class="memItemLeft" align="right" valign="top">virtual const std::vector&lt; std::shared_ptr&lt; <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">Alignment</a> &gt; &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a1d775f9821ce3ecdcdc67cb07f35a4d8">get_alignments</a> () const =0</td></tr>
<tr class="memdesc:a1d775f9821ce3ecdcdc67cb07f35a4d8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return the computed alignments.  <a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a1d775f9821ce3ecdcdc67cb07f35a4d8">More...</a><br /></td></tr>
<tr class="separator:a1d775f9821ce3ecdcdc67cb07f35a4d8"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9f7f056a269c32c909a9bfb7132ba439"><td class="memItemLeft" align="right" valign="top"><a id="a9f7f056a269c32c909a9bfb7132ba439"></a>
virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">reset</a> ()=0</td></tr>
<tr class="memdesc:a9f7f056a269c32c909a9bfb7132ba439"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset aligner object. <br /></td></tr>
<tr class="separator:a9f7f056a269c32c909a9bfb7132ba439"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>CUDA <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html" title="Alignment - Object encapsulating an alignment between 2 string.">Alignment</a> object </p>
</div><h2 class="groupheader">Member Function Documentation</h2>
<a id="adc32085da2b5681f0045d05c43a35f92"></a>
<h2 class="memtitle"><span class="permalink"><a href="#adc32085da2b5681f0045d05c43a35f92">&#9670;&nbsp;</a></span>add_alignment()</h2>

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          <td class="memname">virtual <a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> claragenomics::cudaaligner::Aligner::add_alignment </td>
          <td>(</td>
          <td class="paramtype">const char *&#160;</td>
          <td class="paramname"><em>query</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int32_t&#160;</td>
          <td class="paramname"><em>query_length</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const char *&#160;</td>
          <td class="paramname"><em>target</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int32_t&#160;</td>
          <td class="paramname"><em>target_length</em>&#160;</td>
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          <td>)</td>
          <td></td><td></td>
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<p>Add new alignment object. Only strings with characters from the alphabet [ACGT] are guaranteed to provide correct results. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">query</td><td>Query string </td></tr>
    <tr><td class="paramname">query_length</td><td>Query string length </td></tr>
    <tr><td class="paramname">target</td><td>Target string </td></tr>
    <tr><td class="paramname">target_length</td><td>Target string length </td></tr>
  </table>
  </dd>
</dl>

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<a id="a8b3c20782b9eaa4c2219fb7ff51772db"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8b3c20782b9eaa4c2219fb7ff51772db">&#9670;&nbsp;</a></span>align_all()</h2>

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          <td class="memname">virtual <a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> claragenomics::cudaaligner::Aligner::align_all </td>
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<p>Launch CUDA accelerated alignment. </p>
<p>Perform alignment on all <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html" title="Alignment - Object encapsulating an alignment between 2 string.">Alignment</a> objects previously inserted. This is an async call, and returns before alignment is fully finished. To sync the alignments, refer to the <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482" title="Waits for CUDA accelerated alignment to finish.">sync_alignments()</a> call; To </p>

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<a id="a1d775f9821ce3ecdcdc67cb07f35a4d8"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a1d775f9821ce3ecdcdc67cb07f35a4d8">&#9670;&nbsp;</a></span>get_alignments()</h2>

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          <td class="memname">virtual const std::vector&lt;std::shared_ptr&lt;<a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">Alignment</a>&gt; &gt;&amp; claragenomics::cudaaligner::Aligner::get_alignments </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<p>Return the computed alignments. </p>
<dl class="section return"><dt>Returns</dt><dd>Vector of Alignments. </dd></dl>

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<a id="ac929b7ba836dfac74d8975f652563482"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac929b7ba836dfac74d8975f652563482">&#9670;&nbsp;</a></span>sync_alignments()</h2>

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          <td class="memname">virtual <a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> claragenomics::cudaaligner::Aligner::sync_alignments </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
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<p>Waits for CUDA accelerated alignment to finish. </p>
<p>Blocking call that waits for all the alignments scheduled on the GPU to come to completion. </p>

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<hr/>The documentation for this class was generated from the following file:<ul>
<li>cudaaligner/include/claragenomics/cudaaligner/<a class="el" href="aligner_8hpp_source.html">aligner.hpp</a></li>
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